Multiple sclerosis (MS) is a neurodegenerative autoimmune disease affecting more than 2.5 million people worldwide. Historically, the disease has been described as a ‘white matter’ disease, disintegrating the myelin sheath of neuronal axons. However, new evidence indicates that a concurrent and equally debilitating pathology exists in the ‘grey matter’ or neuronal cell bodies of the central nervous system.Drugs used in the treatment of MS are largely immunosuppressant in nature. They lack a definitive target in the amelioration of the disease and have many side effects. There is a need for a new class of targeted therapeutic agents that have the potential to arrest the disease at the stage at which it is diagnosed. An understanding of the structure and function of the blood-brain barrier (BBB) is crucial to this as it serves as a gateway into the CNS for the brain reactive cells of the immune system. In this study, using a phage display library in combination with an in-vivo panning technique, we were able to isolate brain specific bacteriophage clones. One in particular, named EB1, was characterised as being disease specific and grey matter specific. The unique peptide sequence of clone EB1 was used to synthesise a biotinylated peptide and was subsequently used to characterise its binding pattern in the brain. While attempts to further characterise and isolate the receptor to which this peptide binds are still in progress, we can confirm that the approach has potential for the identification of novel molecular targets for MS therapy and/or drug delivery